diff --git a/Makefile b/Makefile
index f6cbf526..536672c4 100644
--- a/Makefile
+++ b/Makefile
@@ -5,7 +5,7 @@
 KUBECONFIG = $(shell pwd)/metal/kubeconfig.yaml
 KUBE_CONFIG_PATH = $(KUBECONFIG)
 
-default: metal bootstrap external smoke-test post-install clean
+default: metal system external smoke-test post-install clean
 
 configure:
 	./scripts/configure
@@ -14,8 +14,8 @@ configure:
 metal:
 	make -C metal
 
-bootstrap:
-	make -C bootstrap
+system:
+	make -C system
 
 external:
 	make -C external
@@ -48,10 +48,6 @@ test:
 clean:
 	docker compose --project-directory ./metal/roles/pxe_server/files down
 
-dev:
-	make -C metal cluster env=dev
-	make -C bootstrap
-
 docs:
 	mkdocs serve
 
diff --git a/bootstrap/Makefile b/bootstrap/Makefile
deleted file mode 100644
index fa29123f..00000000
--- a/bootstrap/Makefile
+++ /dev/null
@@ -1,15 +0,0 @@
-.POSIX:
-
-default: namespace argocd root
-
-namespace:
-	kubectl create namespace argocd --dry-run=client --output=yaml \
-		| kubectl apply -f -
-
-.PHONY: argocd
-argocd:
-	cd argocd && ./apply.sh
-
-.PHONY: root
-root:
-	cd root && ./apply.sh
diff --git a/bootstrap/argocd/apply.sh b/bootstrap/argocd/apply.sh
deleted file mode 100755
index 702f22b8..00000000
--- a/bootstrap/argocd/apply.sh
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/bin/sh
-
-VALUES="values.yaml"
-
-kubectl get ingress argocd-server --namespace argocd \
-    || VALUES="values-seed.yaml"
-
-helm template \
-    --dependency-update \
-    --include-crds \
-    --namespace argocd \
-    --values "${VALUES}" \
-    argocd . \
-    | kubectl apply -n argocd -f -
-
-kubectl -n argocd wait --timeout=60s --for condition=Established \
-       crd/applications.argoproj.io \
-       crd/applicationsets.argoproj.io
diff --git a/bootstrap/argocd/values-seed.yaml b/bootstrap/argocd/values-seed.yaml
deleted file mode 100644
index f8ead7da..00000000
--- a/bootstrap/argocd/values-seed.yaml
+++ /dev/null
@@ -1,12 +0,0 @@
-argo-cd:
-  server:
-    metrics: &metrics
-      enabled: false
-      serviceMonitor:
-        enabled: false
-  controller:
-    metrics: *metrics
-  repoServer:
-    metrics: *metrics
-  redis:
-    metrics: *metrics
diff --git a/bootstrap/argocd/values.yaml b/bootstrap/argocd/values.yaml
deleted file mode 100644
index 14e5f887..00000000
--- a/bootstrap/argocd/values.yaml
+++ /dev/null
@@ -1,31 +0,0 @@
-argo-cd:
-  global:
-    domain: argocd.khuedoan.com
-  configs:
-    params:
-      server.insecure: true
-      controller.diff.server.side: true
-    cm:
-      resource.ignoreResourceUpdatesEnabled: true
-      resource.customizations.ignoreResourceUpdates.all: |
-        jsonPointers:
-          - /status
-  server:
-    ingress:
-      enabled: true
-      ingressClassName: nginx
-      annotations:
-        cert-manager.io/cluster-issuer: letsencrypt-prod
-      tls: true
-    metrics: &metrics
-      enabled: true
-      serviceMonitor:
-        enabled: true
-  dex:
-    enabled: false
-  controller:
-    metrics: *metrics
-  repoServer:
-    metrics: *metrics
-  redis:
-    metrics: *metrics
diff --git a/bootstrap/main.yml b/bootstrap/main.yml
deleted file mode 100644
index 847ad96b..00000000
--- a/bootstrap/main.yml
+++ /dev/null
@@ -1 +0,0 @@
-# TODO convert ./argocd/apply.sh and ./root/apply.sh to Ansible playbook
diff --git a/bootstrap/root/Chart.yaml b/bootstrap/root/Chart.yaml
deleted file mode 100644
index 563e5408..00000000
--- a/bootstrap/root/Chart.yaml
+++ /dev/null
@@ -1,3 +0,0 @@
-apiVersion: v2
-name: root
-version: 0.0.0
diff --git a/bootstrap/root/apply.sh b/bootstrap/root/apply.sh
deleted file mode 100755
index 2dd4465f..00000000
--- a/bootstrap/root/apply.sh
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/bin/sh
-
-VALUES="values.yaml"
-
-kubectl get ingress gitea --namespace gitea \
-    || VALUES="values-seed.yaml"
-
-helm template \
-    --include-crds \
-    --namespace argocd \
-    --values "${VALUES}" \
-    argocd . \
-    | kubectl apply -n argocd -f -
diff --git a/bootstrap/root/templates/stack.yaml b/bootstrap/root/templates/stack.yaml
deleted file mode 100644
index b16dbd1f..00000000
--- a/bootstrap/root/templates/stack.yaml
+++ /dev/null
@@ -1,41 +0,0 @@
-{{- range $index, $stack := .Values.stacks }}
----
-apiVersion: argoproj.io/v1alpha1
-kind: ApplicationSet
-metadata:
-  name: {{ $stack.name }}
-  namespace: {{ $.Release.Namespace }}
-spec:
-  generators:
-    - git:
-        repoURL: {{ $.Values.gitops.repo }}
-        revision: {{ $.Values.gitops.revision }}
-        directories:
-          - path: {{ $stack.name }}/*
-  template:
-    metadata:
-      name: '{{ `{{path.basename}}` }}'
-    spec:
-      destination:
-        name: in-cluster
-        namespace: '{{ default `{{path.basename}}` $stack.namespace }}'
-      project: default # TODO
-      source:
-        repoURL: {{ $.Values.gitops.repo }}
-        path: '{{ `{{path}}` }}'
-        targetRevision: {{ $.Values.gitops.revision }}
-      syncPolicy:
-        automated:
-          prune: true
-          selfHeal: true
-        retry:
-          limit: 10
-          backoff:
-            duration: 1m
-            factor: 2
-            maxDuration: 16m
-        syncOptions:
-          - CreateNamespace=true
-          - ApplyOutOfSyncOnly=true
-          - ServerSideApply=true
-{{- end }}
diff --git a/bootstrap/root/values-seed.yaml b/bootstrap/root/values-seed.yaml
deleted file mode 100644
index ae729830..00000000
--- a/bootstrap/root/values-seed.yaml
+++ /dev/null
@@ -1,2 +0,0 @@
-gitops:
-  repo: https://github.com/khuedoan/homelab
diff --git a/bootstrap/root/values.yaml b/bootstrap/root/values.yaml
deleted file mode 100644
index 37e96eec..00000000
--- a/bootstrap/root/values.yaml
+++ /dev/null
@@ -1,9 +0,0 @@
-gitops:
-  repo: http://gitea-http.gitea:3000/ops/homelab
-  revision: master
-stacks:
-  - name: bootstrap
-    namespace: argocd  # Override default value
-  - name: system
-  - name: platform
-  - name: apps
diff --git a/docs/reference/architecture/overview.md b/docs/reference/architecture/overview.md
index 55352557..e0159d1b 100644
--- a/docs/reference/architecture/overview.md
+++ b/docs/reference/architecture/overview.md
@@ -10,8 +10,6 @@
 |--------------|       +------------+
 |   ./system   |- - - -| ./external |
 |--------------|       +------------+
-| ./bootstrap  |
-|--------------|
 |   ./metal    |
 |--------------|
 |   HARDWARE   |
@@ -21,7 +19,6 @@
 Main components:
 
 - `./metal`: bare metal management, install Linux and Kubernetes
-- `./bootstrap`: GitOps bootstrap with ArgoCD
 - `./system`: critical system components for the cluster (load balancer, storage, ingress, operation tools...)
 - `./platform`: essential components for service hosting platform (git, build runners, dashboards...)
 - `./apps`: user facing applications
@@ -41,15 +38,11 @@ Everything is automated, after you edit the configuration files, you just need t
     - Create an ephemeral, stateless PXE server
     - Install Linux on all servers in parallel
     - Build a Kubernetes cluster (based on k3s)
-- (2) Build the `./bootstrap` layer:
-    - Install ArgoCD
-    - Configure the root app to manage other layers (and also manage itself)
-
-From now on, ArgoCD will do the rest:
-
-- (3) Build the `./system` layer (storage, networking, monitoring, etc)
-- (4) Build the `./platform` layer (Gitea, Grafana, SSO, etc)
-- (5) Build the `./apps` layer: (Syncthing, Jellyfin, etc)
+- (2) Bootstrap the `./system` layer:
+    - Install ArgoCD and the root app to manage itself and other layers, from now on ArgoCD will do the rest
+    - Install the remaining components (storage, monitoring, etc)
+- (3) Build the `./platform` layer (Gitea, Grafana, SSO, etc)
+- (4) Deploy applications in the `./apps` layer
 
 ```mermaid
 flowchart TD
@@ -57,11 +50,8 @@ flowchart TD
     pxe[PXE Server] -.-> linux[Fedora Server] --> k3s
   end
 
-  subgraph bootstrap[./bootstrap]
-    argocd[ArgoCD] --> rootapp[Root app]
-  end
-
   subgraph system[./system]
+    argocd[ArgoCD and root app]
     nginx[NGINX]
     rook-ceph[Rook Ceph]
     cert-manager
@@ -79,96 +69,18 @@ flowchart TD
   cloudflare -.-> external-dns
   cloudflare -.-> cloudflared
 
-  subgraph platform
+  subgraph platform[./platform]
     Gitea
     Woodpecker
     Grafana
   end
 
-  subgraph apps
+  subgraph apps[./apps]
     homepage[Homepage]
     jellyfin[Jellyfin]
     matrix[Matrix]
     paperless[Paperless]
   end
 
-  make[Run make] -- 1 --> metal -- 2 --> bootstrap -. 3 .-> system -. 4 .-> platform -. 5 .-> apps
+  make[Run make] -- 1 --> metal -- 2 --> system -. 3 .-> platform -. 4 .-> apps
 ```
-
-Below is the pseudo code for the entire process, you don't have to read it right now, but it will be handy for debugging.
-
-??? detailed "Detailed provisioning flow"
-
-    ```
-    Human run make:
-        build ./metal:
-            install the OS:
-                download the installer image and extract it
-                create a PXE server on the controller using Docker Compose:
-                    DHCP server
-                    TFTP server
-                    HTTP server
-                create init config for each machine
-                turn the machines on via WoL
-                the machines boot:
-                    select network boot automatically
-                    broadcast DHCP request
-                    DHCP server reply:
-                        machine IP
-                        TFTP server (next-server) IP
-                    get boot files from TFTP server
-                        GRUB
-                        GRUB config with URL to init config based on MAC address
-                        kernel
-                        initrd
-                    boot to the kernel
-                    download from HTTP server:
-                        init config from the URL in GRUB config
-                        remaining files required to boot
-                    install the OS based on the init config:
-                        configure the system
-                        remaining files required to install
-                    reboot to the new OS
-                controller see the machines are ready
-            build a Kubernetes cluster:
-                download k3s binary
-                generate cluster token
-                copy k3s config files
-                enable k3s service and form a cluster
-                create KUBECONFIG file
-                install Cilium
-        build ./bootstrap:
-            install ArgoCD:
-                apply helm chart
-                wait for status
-            install root app:
-                select values file:
-                    if Gitea unreachable (first install):
-                        get data from GitHub
-                    else:
-                        get data from Gitea
-                apply helm chart
-                wait for status
-    ArgoCD apply the rest:
-        clone git repo
-        install components based on directories:
-            ./bootstrap (it manages itself):
-                argocd
-                root
-            ./system:
-                storage
-                loadbalancer
-                ingress
-                etc
-            ./platform (depends on ./system):
-                git:
-                    migrate the homelab repository from GitHub
-                    ArgoCD switch the source from GitHub to Gitea
-                ci
-                dashboards
-                etc
-            ./apps (depends on ./system and ./platform):
-                homepage
-                jellyfin
-                etc
-    ```
diff --git a/scripts/configure b/scripts/configure
index a53a6f09..a93ba3dd 100755
--- a/scripts/configure
+++ b/scripts/configure
@@ -57,7 +57,6 @@ def main() -> None:
         paths=[
             ".ci",
             "apps",
-            "bootstrap",
             "platform",
             "system",
             "external"
@@ -68,7 +67,7 @@ def main() -> None:
         pattern=upstream_config['seed_repo'],
         replacement=seed_repo,
         paths=[
-            "bootstrap",
+            "system",
             "platform"
         ]
     )
diff --git a/system/Makefile b/system/Makefile
new file mode 100644
index 00000000..2fbf29f0
--- /dev/null
+++ b/system/Makefile
@@ -0,0 +1,8 @@
+.POSIX:
+
+export KUBECONFIG = $(shell pwd)/../metal/kubeconfig.yaml
+
+.PHONY: bootstrap
+bootstrap:
+	ansible-playbook \
+		bootstrap.yml
diff --git a/bootstrap/argocd/Chart.yaml b/system/argocd/Chart.yaml
similarity index 60%
rename from bootstrap/argocd/Chart.yaml
rename to system/argocd/Chart.yaml
index e0b86840..c3b2c050 100644
--- a/bootstrap/argocd/Chart.yaml
+++ b/system/argocd/Chart.yaml
@@ -5,3 +5,6 @@ dependencies:
   - name: argo-cd
     version: 6.4.1
     repository: https://argoproj.github.io/argo-helm
+  - name: argocd-apps
+    version: 2.0.0
+    repository: https://argoproj.github.io/argo-helm
diff --git a/system/argocd/values-seed.yaml b/system/argocd/values-seed.yaml
new file mode 100644
index 00000000..4e8b3c90
--- /dev/null
+++ b/system/argocd/values-seed.yaml
@@ -0,0 +1,28 @@
+argo-cd:
+  server:
+    metrics: &metrics
+      enabled: false
+      serviceMonitor:
+        enabled: false
+  controller:
+    metrics: *metrics
+  repoServer:
+    metrics: *metrics
+  redis:
+    metrics: *metrics
+argocd-apps:
+  applicationsets:
+    root:
+      generators:
+        - git:
+            repoURL: &repoURL https://github.com/khuedoan/homelab
+            revision: &revision master
+            directories:
+              - path: system/*
+              - path: platform/*
+              - path: apps/*
+      template:
+        spec:
+          source:
+            repoURL: *repoURL
+            targetRevision: *revision
diff --git a/system/argocd/values.yaml b/system/argocd/values.yaml
new file mode 100644
index 00000000..1797ae3d
--- /dev/null
+++ b/system/argocd/values.yaml
@@ -0,0 +1,69 @@
+argo-cd:
+  global:
+    domain: argocd.khuedoan.com
+  configs:
+    params:
+      server.insecure: true
+      controller.diff.server.side: true
+    cm:
+      resource.ignoreResourceUpdatesEnabled: true
+      resource.customizations.ignoreResourceUpdates.all: |
+        jsonPointers:
+          - /status
+  server:
+    ingress:
+      enabled: true
+      ingressClassName: nginx
+      annotations:
+        cert-manager.io/cluster-issuer: letsencrypt-prod
+      tls: true
+    metrics: &metrics
+      enabled: true
+      serviceMonitor:
+        enabled: true
+  dex:
+    enabled: false
+  controller:
+    metrics: *metrics
+  repoServer:
+    metrics: *metrics
+  redis:
+    metrics: *metrics
+argocd-apps:
+  applicationsets:
+    root:
+      namespace: argocd
+      generators:
+        - git:
+            repoURL: &repoURL http://gitea-http.gitea:3000/ops/homelab
+            revision: &revision master
+            directories:
+              - path: system/*
+              - path: platform/*
+              - path: apps/*
+      template:
+        metadata:
+          name: '{{path.basename}}'
+        spec:
+          destination:
+            name: in-cluster
+            namespace: '{{path.basename}}'
+          project: default  # TODO
+          source:
+            repoURL: *repoURL
+            path: '{{path}}'
+            targetRevision: *revision
+          syncPolicy:
+            automated:
+              prune: true
+              selfHeal: true
+            retry:
+              limit: 10
+              backoff:
+                duration: 1m
+                factor: 2
+                maxDuration: 16m
+            syncOptions:
+              - CreateNamespace=true
+              - ApplyOutOfSyncOnly=true
+              - ServerSideApply=true
diff --git a/system/bootstrap.yml b/system/bootstrap.yml
new file mode 100644
index 00000000..37d5c1b7
--- /dev/null
+++ b/system/bootstrap.yml
@@ -0,0 +1,36 @@
+- name: Bootstrapping the cluster
+  hosts: localhost
+  tasks:
+    - name: Create ArgoCD namespace
+      kubernetes.core.k8s:
+        api_version: v1
+        kind: Namespace
+        name: argocd
+        state: present
+
+    - name: Check if this is the first installation
+      kubernetes.core.k8s_info:
+        kind: Pod
+        label_selectors:
+          - app.kubernetes.io/instance=gitea
+        field_selectors:
+          - status.phase=Running
+      register: first_install
+
+    - name: Render ArgoCD manifests from Helm chart
+      kubernetes.core.helm_template:
+        chart_ref: ./argocd
+        include_crds: true
+        release_name: argocd
+        release_namespace: argocd
+        dependency_update: true
+        values_files:
+          - "argocd/{{ (first_install.resources | length == 0) | ternary('values-seed.yaml', 'values.yaml') }}"
+      register: argocd_manifests
+
+    - name: Apply ArgoCD manifests
+      kubernetes.core.k8s:
+        resource_definition: "{{ argocd_manifests.stdout }}"
+        apply: true
+        server_side_apply:
+          field_manager: argocd-controller